//
//  Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <list>
#include <algorithm>
#include <math.h>
#include "../QueryAtom.h"
#include "../QueryBond.h"
#include "../SmilesParse/SmilesWrite.h"
#include "../SmilesParse/SmartsWrite.h"
#include "../SmilesParse/SmilesParse.h"
#include "../Substruct/SubstructMatch.h"
#include "SubstructMatchCustom.h"
#include "MaximumCommonSubgraph.h"

namespace RDKit {
namespace FMCS {

struct LabelDefinition {
  unsigned ItemIndex;  // item with this label value
  unsigned Value;
  LabelDefinition() : ItemIndex(NotSet), Value(NotSet) {}
  LabelDefinition(unsigned i, unsigned value) : ItemIndex(i), Value(value) {}
};

MaximumCommonSubgraph::MaximumCommonSubgraph(const MCSParameters* params) {
  Parameters = (0 != params ? *params : MCSParameters());
  if (!Parameters.ProgressCallback) {
    Parameters.ProgressCallback = MCSProgressCallbackTimeout;
    Parameters.ProgressCallbackUserData = &To;
  }
  if (Parameters.AtomCompareParameters.MatchChiralTag &&
      0 == Parameters.FinalMatchChecker) {
    Parameters.FinalMatchChecker = FinalChiralityCheckFunction;
    Parameters.BondCompareParameters.MatchStereo = true;
  }
  To = nanoClock();
}

static bool molPtr_NumBondLess(
    const ROMol* l,
    const ROMol* r) {  // need for sorting the source molecules by size
  return l->getNumBonds() < r->getNumBonds();
}

void MaximumCommonSubgraph::init() {
  QueryMolecule = Molecules.front();

  Targets.clear();
#ifdef FAST_SUBSTRUCT_CACHE
  QueryAtomLabels.clear();
  QueryBondLabels.clear();
  QueryAtomMatchTable.clear();
  QueryBondMatchTable.clear();
  RingMatchTables.clear();
#endif
#ifdef DUP_SUBSTRUCT_CACHE
  DuplicateCache.clear();
#endif
  void* userData = Parameters.CompareFunctionsUserData;

  if (Parameters.BondCompareParameters.CompleteRingsOnly ||
      Parameters.BondCompareParameters.RingMatchesRingOnly) {
#ifdef FAST_SUBSTRUCT_CACHE
    RingMatchTables.init(QueryMolecule);
    Parameters.CompareFunctionsUserData = &RingMatchTables;
#endif
  }
  size_t nq = 0;
#ifdef FAST_SUBSTRUCT_CACHE
  // fill out RingMatchTables to check cache Hash collision by checking match a
  // part of Query to Query
  if (!userData  // predefined functor - compute RingMatchTable for all targets
      && (Parameters.BondCompareParameters.CompleteRingsOnly ||
          Parameters.BondCompareParameters.RingMatchesRingOnly))
    RingMatchTables.computeRingMatchTable(QueryMolecule, QueryMolecule,
                                          Parameters);

  // fill out match tables
  nq = QueryMolecule->getNumAtoms();
  QueryAtomMatchTable.resize(nq, nq);
  for (size_t aj = 0; aj < nq; aj++)
    for (size_t ai = 0; ai < nq; ai++)
      QueryAtomMatchTable.set(
          ai, aj, Parameters.AtomTyper(Parameters.AtomCompareParameters,
                                       *QueryMolecule, ai, *QueryMolecule, aj,
                                       Parameters.CompareFunctionsUserData));

  nq = QueryMolecule->getNumBonds();
  QueryBondMatchTable.resize(nq, nq);
  for (size_t aj = 0; aj < nq; aj++)
    for (size_t ai = 0; ai < nq; ai++)
      QueryBondMatchTable.set(
          ai, aj, Parameters.BondTyper(Parameters.BondCompareParameters,
                                       *QueryMolecule, ai, *QueryMolecule, aj,
                                       Parameters.CompareFunctionsUserData));
  // Compute label values based on current functor and parameters for code
  // Morgan correct computation.
  unsigned currentLabelValue = 1;
  std::vector<LabelDefinition> labels;
  nq = QueryMolecule->getNumAtoms();
  QueryAtomLabels.resize(nq);
  for (size_t ai = 0; ai < nq; ai++) {
    if (MCSAtomCompareAny ==
        Parameters
            .AtomTyper)  // predefined functor without atom compare parameters
      QueryAtomLabels[ai] = 1;
    else {
      const Atom* atom = QueryMolecule->getAtomWithIdx(ai);
      if (MCSAtomCompareElements ==
          Parameters
              .AtomTyper)  // predefined functor without atom compare parameters
        QueryAtomLabels[ai] = atom->getAtomicNum() |
                              (Parameters.AtomCompareParameters.MatchValences
                                   ? (atom->getTotalValence() >> 8)
                                   : 0);
      else if (MCSAtomCompareIsotopes ==
               Parameters.AtomTyper)  // predefined functor without atom compare
                                      // parameters
        QueryAtomLabels[ai] = atom->getAtomicNum() | (atom->getIsotope() >> 8) |
                              (Parameters.AtomCompareParameters.MatchValences
                                   ? (atom->getTotalValence() >> 16)
                                   : 0);
      else {  // custom user defined functor
        QueryAtomLabels[ai] = NotSet;
        for (size_t i = 0; i < labels.size(); i++)
          if (Parameters.AtomTyper(Parameters.AtomCompareParameters,
                                   *QueryMolecule, labels[i].ItemIndex,
                                   *QueryMolecule, ai,
                                   userData)) {  // equal itoms
            QueryAtomLabels[ai] = labels[i].Value;
            break;
          }
        if (NotSet == QueryAtomLabels[ai]) {  // not found -> create new label
          QueryAtomLabels[ai] = ++currentLabelValue;
          labels.push_back(LabelDefinition(ai, currentLabelValue));
        }
      }
    }
  }
  labels.clear();
  currentLabelValue = 1;
  nq = QueryMolecule->getNumBonds();
  QueryBondLabels.resize(nq);
  for (size_t aj = 0; aj < nq; aj++) {
    const Bond* bond = QueryMolecule->getBondWithIdx(aj);
    unsigned ring = 0;
    if (Parameters.BondCompareParameters.CompleteRingsOnly ||
        Parameters.BondCompareParameters.RingMatchesRingOnly) {
      ring = RingMatchTables.isQueryBondInRing(aj) ? 0 : 1;  // is bond in ring
    }
    if (MCSBondCompareAny ==
        Parameters
            .BondTyper)  // predefined functor without atom compare parameters
      QueryBondLabels[aj] = 1 | (ring >> 8);
    else if (MCSBondCompareOrderExact ==
             Parameters
                 .BondTyper)  // predefined functor without compare parameters
      QueryBondLabels[aj] = (bond->getBondType() + 1) | (ring >> 8);
    else if (MCSBondCompareOrder ==
             Parameters
                 .BondTyper) {  // predefined functor, ignore Aromatization
      unsigned order = bond->getBondType();
      if (Bond::AROMATIC == order ||
          Bond::ONEANDAHALF == order)  // ignore Aromatization
        order = Bond::SINGLE;
      else if (Bond::TWOANDAHALF == order)
        order = Bond::DOUBLE;
      else if (Bond::THREEANDAHALF == order)
        order = Bond::TRIPLE;
      else if (Bond::FOURANDAHALF == order)
        order = Bond::QUADRUPLE;
      else if (Bond::FIVEANDAHALF == order)
        order = Bond::QUINTUPLE;
      QueryBondLabels[aj] = (order + 1) | (ring >> 8);
    } else {  // custom user defined functor
      QueryBondLabels[aj] = NotSet;
      for (size_t i = 0; i < labels.size(); i++)
        if (Parameters.BondTyper(Parameters.BondCompareParameters,
                                 *QueryMolecule, labels[i].ItemIndex,
                                 *QueryMolecule, aj,
                                 userData)) {  // equal bonds + ring ...
          QueryBondLabels[aj] = labels[i].Value;
          break;
        }
      if (NotSet == QueryAtomLabels[aj]) {  // not found -> create new label
        QueryBondLabels[aj] = ++currentLabelValue;
        labels.push_back(LabelDefinition(aj, currentLabelValue));
      }
    }
  }
#endif
  Targets.resize(Molecules.size() - 1);
  size_t i = 0;
  for (std::vector<const ROMol*>::iterator it = Molecules.begin() + 1;
       it != Molecules.end(); it++, i++) {
    Targets[i].Molecule = *it;
    // build Target Topology ADD ATOMs
    size_t j = 0;  // current item
    for (ROMol::ConstAtomIterator a = Targets[i].Molecule->beginAtoms();
         a != Targets[i].Molecule->endAtoms(); a++, j++) {
      Targets[i].Topology.addAtom((*a)->getIdx());
    }
    // build Target Topology ADD BONDs
    for (ROMol::ConstBondIterator b = Targets[i].Molecule->beginBonds();
         b != Targets[i].Molecule->endBonds(); b++) {
      const Bond* bond = *b;
      unsigned ii = bond->getBeginAtomIdx();
      unsigned jj = bond->getEndAtomIdx();
      Targets[i].Topology.addBond((*b)->getIdx(), ii, jj);
    }

    // fill out RingMatchTables
    if (!userData  // predefined functor - compute RingMatchTable for all
                   // targets
        &&
        (Parameters.BondCompareParameters.CompleteRingsOnly ||
         Parameters.BondCompareParameters.RingMatchesRingOnly)) {
#ifdef FAST_SUBSTRUCT_CACHE
      RingMatchTables.addTargetBondRingsIndeces(Targets[i].Molecule);
      RingMatchTables.computeRingMatchTable(QueryMolecule, Targets[i].Molecule,
                                            Parameters);
#endif
    }

    // fill out match tables
    size_t nq = QueryMolecule->getNumAtoms();
    size_t nt = (*it)->getNumAtoms();
    Targets[i].AtomMatchTable.resize(nq, nt);

    for (size_t aj = 0; aj < nt; aj++)
      for (size_t ai = 0; ai < nq; ai++)
        Targets[i].AtomMatchTable.set(
            ai, aj,
            Parameters.AtomTyper(Parameters.AtomCompareParameters,
                                 *QueryMolecule, ai, *Targets[i].Molecule, aj,
                                 Parameters.CompareFunctionsUserData));

    nq = QueryMolecule->getNumBonds();
    nt = (*it)->getNumBonds();
    Targets[i].BondMatchTable.resize(nq, nt);
    for (size_t aj = 0; aj < nt; aj++)
      for (size_t ai = 0; ai < nq; ai++)
        Targets[i].BondMatchTable.set(
            ai, aj,
            Parameters.BondTyper(Parameters.BondCompareParameters,
                                 *QueryMolecule, ai, *Targets[i].Molecule, aj,
                                 Parameters.CompareFunctionsUserData));
  }

  Parameters.CompareFunctionsUserData = userData;  // restore
}

struct QueryRings {
  std::vector<unsigned> BondRings;  // amount of rings
  std::vector<unsigned> AtomRings;  // amount of rings

  QueryRings(const ROMol* query)
      : BondRings(query->getNumBonds()), AtomRings(query->getNumAtoms()) {
    {
      for (size_t b = 0; b < BondRings.size(); b++) BondRings[b] = 0;
      const RingInfo::VECT_INT_VECT& rings = query->getRingInfo()->bondRings();
      for (RingInfo::VECT_INT_VECT::const_iterator r = rings.begin();
           r != rings.end(); r++)
        for (INT_VECT::const_iterator ri = r->begin(); ri != r->end(); ri++)
          ++BondRings[*ri];
    }
    {
      for (size_t a = 0; a < AtomRings.size(); a++) AtomRings[a] = 0;
      const RingInfo::VECT_INT_VECT& rings = query->getRingInfo()->atomRings();
      for (RingInfo::VECT_INT_VECT::const_iterator r = rings.begin();
           r != rings.end(); r++)
        for (INT_VECT::const_iterator ri = r->begin(); ri != r->end(); ri++)
          ++AtomRings[*ri];
    }
  }

  inline unsigned getNumberRings(const Bond* bond) const {
    return BondRings[bond->getIdx()];
  }

  inline unsigned getNumberRings(const Atom* atom) const {
    return AtomRings[atom->getIdx()];
  }
};

struct WeightedBond {
  const Bond* BondPtr;
  unsigned Weight;
  WeightedBond() : BondPtr(0), Weight(0) {}
  WeightedBond(const Bond* bond, const QueryRings& r)
      : BondPtr(bond), Weight(0) {
    // score ((bond.is_in_ring + atom1.is_in_ring + atom2.is_in_ring)
    if (r.getNumberRings(bond)) Weight += 1;
    if (r.getNumberRings(bond->getBeginAtom())) Weight += 1;
    if (r.getNumberRings(bond->getEndAtom())) Weight += 1;
  }
  bool operator<(const WeightedBond& r) {
    return Weight >= r.Weight;  // sort in Z-A order (Rings first)
  }
};

void MaximumCommonSubgraph::makeInitialSeeds() {
  // build a set of initial seeds as "all" single bonds from query molecule
  std::vector<bool> excludedBonds(QueryMolecule->getNumBonds());
  for (size_t i = 0; i < excludedBonds.size(); i++) excludedBonds[i] = false;

  Seeds.clear();
  QueryMoleculeMatchedBonds = 0;
  QueryMoleculeMatchedAtoms = 0;
  if (!Parameters.InitialSeed.empty()) {  // make user defined seed
    std::auto_ptr<const ROMol> initialSeedMolecule(
        (const ROMol*)SmartsToMol(Parameters.InitialSeed));
    // make a set of of seed as indeces and pointers to current query molecule
    // items based on matching results
    std::vector<MatchVectType> matching_substructs;
    SubstructMatch(*QueryMolecule, *initialSeedMolecule, matching_substructs);
    // loop throw all fragments of Query matched to initial seed
    for (std::vector<MatchVectType>::const_iterator ms =
             matching_substructs.begin();
         ms != matching_substructs.end(); ms++) {
      Seed seed;
      seed.ExcludedBonds = excludedBonds;
      seed.MatchResult.resize(Targets.size());
#ifdef VERBOSE_STATISTICS_ON
      {
        ++VerboseStatistics.Seed;
        ++VerboseStatistics.InitialSeed;
      }
#endif
      // add all matched atoms of the matched query fragment
      std::map<unsigned, unsigned> initialSeedToQueryAtom;
      for (MatchVectType::const_iterator msb = ms->begin(); msb != ms->end();
           msb++) {
        unsigned qai = msb->second;
        unsigned sai = msb->first;
        seed.addAtom(QueryMolecule->getAtomWithIdx(qai));
        initialSeedToQueryAtom[sai] = qai;
      }
      // add all bonds (existed in initial seed !!!) between all matched atoms
      // in query
      for (MatchVectType::const_iterator msb = ms->begin(); msb != ms->end();
           msb++) {
        const Atom* atom = initialSeedMolecule->getAtomWithIdx(msb->first);
        ROMol::OEDGE_ITER beg, end;
        for (boost::tie(beg, end) = initialSeedMolecule->getAtomBonds(atom);
             beg != end; beg++) {
          const Bond& initialBond = *((*initialSeedMolecule)[*beg]);
          unsigned qai1 =
              initialSeedToQueryAtom.find(initialBond.getBeginAtomIdx())
                  ->second;
          unsigned qai2 =
              initialSeedToQueryAtom.find(initialBond.getEndAtomIdx())->second;

          const Bond* b = QueryMolecule->getBondBetweenAtoms(qai1, qai2);
          if (!seed.ExcludedBonds[b->getIdx()]) {
            seed.addBond(b);
            seed.ExcludedBonds[b->getIdx()] = true;
          }
        }
      }
      seed.computeRemainingSize(*QueryMolecule);

      if (checkIfMatchAndAppend(seed))
        QueryMoleculeMatchedBonds = seed.getNumBonds();
    }
  } else {  // create a set of seeds from each query bond
    // R1 additional performance OPTIMISATION
    // if(Parameters.BondCompareParameters.CompleteRingsOnly)
    // disable all mismatched rings, and do not generate initial seeds from such
    // disabled bonds
    //  for(  rings .....) for(i......)
    //   if(mismatched) excludedBonds[i.......] = true;
    QueryRings r(QueryMolecule);
    std::vector<WeightedBond> wb;
    wb.reserve(QueryMolecule->getNumBonds());
    for (RWMol::ConstBondIterator bi = QueryMolecule->beginBonds();
         bi != QueryMolecule->endBonds(); bi++)
      wb.push_back(WeightedBond(*bi, r));

    for (std::vector<WeightedBond>::const_iterator bi = wb.begin();
         bi != wb.end(); bi++) {
      // R1 additional performance OPTIMISATION
      // if(excludedBonds[(*bi)->getIdx()])
      //    continue;
      Seed seed;
      seed.MatchResult.resize(Targets.size());

#ifdef VERBOSE_STATISTICS_ON
      {
        ++VerboseStatistics.Seed;
        ++VerboseStatistics.InitialSeed;
      }
#endif
      seed.addAtom(bi->BondPtr->getBeginAtom());
      seed.addAtom(bi->BondPtr->getEndAtom());
      seed.ExcludedBonds = excludedBonds;  // all bonds from first to current
      seed.addBond(bi->BondPtr);
      excludedBonds[bi->BondPtr->getIdx()] = true;

      seed.computeRemainingSize(*QueryMolecule);

      if (checkIfMatchAndAppend(seed)) {
        ++QueryMoleculeMatchedBonds;
      } else {
        // optionally remove all such bonds from all targets TOPOLOGY where it
        // exists.
        //..........

        // disable (mark as already processed) mismatched bond in all seeds
        for (SeedSet::iterator si = Seeds.begin(); si != Seeds.end(); si++)
          si->ExcludedBonds[bi->BondPtr->getIdx()] = true;

#ifdef VERBOSE_STATISTICS_ON
        ++VerboseStatistics.MismatchedInitialSeed;
#endif
      }
    }
  }
  size_t nq = QueryMolecule->getNumAtoms();
  for (size_t i = 0; i < nq; i++) {  // all query's atoms
    unsigned matched = 0;
    for (std::vector<Target>::const_iterator tag = Targets.begin();
         tag != Targets.end(); tag++) {
      size_t nt = tag->Molecule->getNumAtoms();
      for (size_t aj = 0; aj < nt; aj++) {
        if (tag->AtomMatchTable.at(i, aj)) {
          ++matched;
          break;
        }
      }
    }
    if (matched >= ThresholdCount) ++QueryMoleculeMatchedAtoms;
  }
}

bool MaximumCommonSubgraph::growSeeds() {
  bool mcsFound = false;
  bool canceled = false;
  unsigned steps = 99999;  // steps from last progress callback call. call it
                           // immediately in the begining

  // Find MCS -- SDF Seed growing OPTIMISATION (it works in 3 times faster)
  while (!Seeds.empty()) {
    if (getMaxNumberBonds() == QueryMoleculeMatchedBonds)  // MCS == Query
      break;
    ++steps;
#ifdef VERBOSE_STATISTICS_ON
    VerboseStatistics.TotalSteps++;
#endif
    SeedSet::iterator si = Seeds.begin();

    si->grow(*this);
    {
      const Seed& fs = Seeds.front();
      // bigger substructure found
      if (fs.CopyComplete)
        if ((!Parameters.MaximizeBonds &&
             (fs.getNumAtoms() > getMaxNumberAtoms() ||
              (fs.getNumAtoms() == getMaxNumberAtoms() &&
               fs.getNumBonds() > getMaxNumberBonds()))) ||
            (Parameters.MaximizeBonds &&
             (fs.getNumBonds() > getMaxNumberBonds() ||
              (fs.getNumBonds() == getMaxNumberBonds() &&
               fs.getNumAtoms() > getMaxNumberAtoms())))) {
          mcsFound = true;
#ifdef VERBOSE_STATISTICS_ON
          VerboseStatistics.MCSFoundStep = VerboseStatistics.TotalSteps;
          VerboseStatistics.MCSFoundTime = nanoClock();
#endif
          McsIdx.Atoms = fs.MoleculeFragment.Atoms;
          McsIdx.Bonds = fs.MoleculeFragment.Bonds;
          McsIdx.AtomsIdx = fs.MoleculeFragment.AtomsIdx;
          McsIdx.BondsIdx = fs.MoleculeFragment.BondsIdx;
          if (Parameters.Verbose) {
            std::cout << VerboseStatistics.TotalSteps
                      << " Seeds:" << Seeds.size() << " MCS "
                      << McsIdx.Atoms.size() << " atoms, "
                      << McsIdx.Bonds.size() << " bonds";
            printf(" for %.4lf seconds. bond[0]=%u\n",
                   double(VerboseStatistics.MCSFoundTime - To) / 1000000.,
                   McsIdx.BondsIdx[0]);
          }
        }
    }
    if (NotSet == si->GrowingStage)  // finished
      Seeds.erase(si);
    if (Parameters.ProgressCallback && (steps >= 377)) {
      steps = 0;
      Stat.NumAtoms = getMaxNumberAtoms();
      Stat.NumBonds = getMaxNumberBonds();
      if (!Parameters.ProgressCallback(Stat, Parameters,
                                       Parameters.ProgressCallbackUserData)) {
        canceled = true;
        break;
      }
    }
  }

  if (mcsFound) {  // postponed copy of current set of molecules for threshold <
                   // 1.
    McsIdx.QueryMolecule = QueryMolecule;
    McsIdx.Targets = Targets;
  }
  return !canceled;
}

struct AtomMatch {  // for each seed atom (matched)
  unsigned QueryAtomIdx;
  unsigned TargetAtomIdx;
  AtomMatch() : QueryAtomIdx(NotSet), TargetAtomIdx(NotSet) {}
};
typedef std::vector<AtomMatch> AtomMatchSet;

std::string MaximumCommonSubgraph::generateResultSMARTS(
    const MCS& mcsIdx) const {
  // match the result MCS with all targets to check if it is exact match or
  // template
  Seed seed;  // result MCS
  seed.ExcludedBonds.resize(mcsIdx.QueryMolecule->getNumBonds());
  for (size_t i = 0; i < seed.ExcludedBonds.size(); i++)
    seed.ExcludedBonds[i] = false;
  std::vector<AtomMatchSet> atomMatchResult(mcsIdx.Targets.size());
  std::vector<unsigned> atomIdxMap(mcsIdx.QueryMolecule->getNumAtoms());
  std::vector<std::map<unsigned, const Bond*> > bondMatchSet(
      mcsIdx.Bonds.size());  // key is unique BondType
  std::vector<std::map<unsigned, const Atom*> > atomMatchSet(
      mcsIdx.Atoms.size());  // key is unique atomic number

  for (std::vector<const Atom*>::const_iterator atom = mcsIdx.Atoms.begin();
       atom != mcsIdx.Atoms.end(); atom++) {
    atomIdxMap[(*atom)->getIdx()] = seed.getNumAtoms();
    seed.addAtom((*atom));
  }
  for (std::vector<const Bond*>::const_iterator bond = mcsIdx.Bonds.begin();
       bond != mcsIdx.Bonds.end(); bond++)
    seed.addBond((*bond));

  unsigned itarget = 0;
  for (std::vector<Target>::const_iterator tag = mcsIdx.Targets.begin();
       tag != mcsIdx.Targets.end(); tag++, itarget++) {
    match_V_t match;  // THERE IS NO Bonds match INFO !!!!
    bool target_matched = SubstructMatchCustomTable(
        tag->Topology, *tag->Molecule, seed.Topology, *QueryMolecule,
        tag->AtomMatchTable, tag->BondMatchTable, &Parameters, &match);
    if (!target_matched) continue;
    atomMatchResult[itarget].resize(seed.getNumAtoms());
    for (match_V_t::const_iterator mit = match.begin(); mit != match.end();
         mit++) {
      unsigned ai = mit->first;  // SeedAtomIdx
      atomMatchResult[itarget][ai].QueryAtomIdx = seed.Topology[mit->first];
      atomMatchResult[itarget][ai].TargetAtomIdx = tag->Topology[mit->second];
      const Atom* ta =
          tag->Molecule->getAtomWithIdx(tag->Topology[mit->second]);
      if (ta &&
          ta->getAtomicNum() != seed.MoleculeFragment.Atoms[ai]->getAtomicNum())
        atomMatchSet[ai][ta->getAtomicNum()] = ta;  // add
    }
    // AND BUILD BOND MATCH INFO
    unsigned bi = 0;
    for (std::vector<const Bond*>::const_iterator bond = mcsIdx.Bonds.begin();
         bond != mcsIdx.Bonds.end(); bond++, bi++) {
      unsigned i = atomIdxMap[(*bond)->getBeginAtomIdx()];
      unsigned j = atomIdxMap[(*bond)->getEndAtomIdx()];
      unsigned ti = atomMatchResult[itarget][i].TargetAtomIdx;
      unsigned tj = atomMatchResult[itarget][j].TargetAtomIdx;
      const Bond* tb = tag->Molecule->getBondBetweenAtoms(ti, tj);
      if (tb && (*bond)->getBondType() != tb->getBondType())
        bondMatchSet[bi][tb->getBondType()] = tb;  // add
    }
  }

  // Generate result's SMARTS

  RWMol mol;        // create molecule from MCS for MolToSmarts()
  unsigned ai = 0;  // SeedAtomIdx
  for (std::vector<const Atom*>::const_iterator atom = mcsIdx.Atoms.begin();
       atom != mcsIdx.Atoms.end(); atom++, ai++) {
    if (Parameters.AtomTyper ==
        MCSAtomCompareIsotopes) {  // do '[0*]-[0*]-[13*]' for CC[13NH2]
      QueryAtom a;
      a.setQuery(makeAtomIsotopeQuery((int)(*atom)->getIsotope()));
      mol.addAtom(&a, true, false);
    } else {
      QueryAtom a;  // generate [#6] instead of C or c !
      a.setQuery(makeAtomNumQuery((*atom)->getAtomicNum()));
      // for all atomMatchSet[ai] items add atom query to template like
      // [#6,#17,#9, ... ]
      for (std::map<unsigned, const Atom*>::const_iterator am =
               atomMatchSet[ai].begin();
           am != atomMatchSet[ai].end(); am++) {
        a.expandQuery(makeAtomNumQuery(am->second->getAtomicNum()),
                      Queries::COMPOSITE_OR);
        if (Parameters.AtomCompareParameters.MatchChiralTag &&
            (am->second->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
             am->second->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW))
          a.setChiralTag(am->second->getChiralTag());
      }
      mol.addAtom(&a, true, false);
    }
  }
  unsigned bi = 0;  // Seed Idx
  for (std::vector<const Bond*>::const_iterator bond = mcsIdx.Bonds.begin();
       bond != mcsIdx.Bonds.end(); bond++, bi++) {
    QueryBond b;
    unsigned beginAtomIdx = atomIdxMap[(*bond)->getBeginAtomIdx()];
    unsigned endAtomIdx = atomIdxMap[(*bond)->getEndAtomIdx()];
    b.setBeginAtomIdx(beginAtomIdx);
    b.setEndAtomIdx(endAtomIdx);
    b.setQuery(makeBondOrderEqualsQuery((*bond)->getBondType()));
    // add OR template if need
    for (std::map<unsigned, const Bond*>::const_iterator bm =
             bondMatchSet[bi].begin();
         bm != bondMatchSet[bi].end(); bm++) {
      b.expandQuery(makeBondOrderEqualsQuery(bm->second->getBondType()),
                    Queries::COMPOSITE_OR);
      if (Parameters.BondCompareParameters.MatchStereo &&
          (bm->second->getStereo() == Bond::STEREOZ ||
           bm->second->getStereo() == Bond::STEREOE))
        b.setStereo(bm->second->getStereo());
    }
    mol.addBond(&b, false);
  }

  return MolToSmarts(mol, true);
}

bool MaximumCommonSubgraph::createSeedFromMCS(size_t newQueryTarget,
                                              Seed& newSeed) {
  Seed mcs;
  mcs.ExcludedBonds.resize(McsIdx.QueryMolecule->getNumBonds());
  for (size_t i = 0; i < mcs.ExcludedBonds.size(); i++)
    mcs.ExcludedBonds[i] = false;
  std::vector<unsigned> mcsAtomIdxMap(McsIdx.QueryMolecule->getNumAtoms());

  for (std::vector<const Atom*>::const_iterator atom = McsIdx.Atoms.begin();
       atom != McsIdx.Atoms.end(); atom++) {
    mcsAtomIdxMap[(*atom)->getIdx()] = mcs.addAtom((*atom));
  }
  for (std::vector<const Bond*>::const_iterator bond = McsIdx.Bonds.begin();
       bond != McsIdx.Bonds.end(); bond++)
    mcs.addBond((*bond));

  const Target& newQuery = McsIdx.Targets[newQueryTarget];

  match_V_t match;
  bool target_matched = SubstructMatchCustomTable(
      newQuery.Topology, *newQuery.Molecule, mcs.Topology,
      *McsIdx.QueryMolecule, newQuery.AtomMatchTable, newQuery.BondMatchTable,
      &Parameters, &match);
  if (!target_matched) return false;

  AtomMatchSet atomMatchResult(mcs.getNumAtoms());

  newSeed.ExcludedBonds.resize(newQuery.Molecule->getNumBonds());
  for (size_t j = 0; j < newSeed.ExcludedBonds.size(); j++)
    newSeed.ExcludedBonds[j] = false;

  for (match_V_t::const_iterator mit = match.begin(); mit != match.end();
       mit++) {
    unsigned ai = mit->first;  // SeedAtomIdx in mcs seed
    atomMatchResult[ai].QueryAtomIdx = mcs.Topology[mit->first];
    atomMatchResult[ai].TargetAtomIdx = newQuery.Topology[mit->second];
    const Atom* ta =
        newQuery.Molecule->getAtomWithIdx(newQuery.Topology[mit->second]);
    newSeed.addAtom(ta);
  }

  for (std::vector<const Bond*>::const_iterator bond = McsIdx.Bonds.begin();
       bond != McsIdx.Bonds.end(); bond++) {
    unsigned i = mcsAtomIdxMap[(*bond)->getBeginAtomIdx()];
    unsigned j = mcsAtomIdxMap[(*bond)->getEndAtomIdx()];
    unsigned ti = atomMatchResult[i].TargetAtomIdx;
    unsigned tj = atomMatchResult[j].TargetAtomIdx;
    const Bond* tb = newQuery.Molecule->getBondBetweenAtoms(ti, tj);
    newSeed.addBond(tb);
  }
  newSeed.computeRemainingSize(*newQuery.Molecule);
  return true;
}

MCSResult MaximumCommonSubgraph::find(const std::vector<ROMOL_SPTR>& src_mols) {
  clear();
  MCSResult res;

  if (src_mols.size() < 2)
    throw std::runtime_error(
        "FMCS. Invalid argument. mols.size() must be at least 2");
  if (Parameters.Threshold > 1.0)
    throw std::runtime_error(
        "FMCS. Invalid argument. Parameter Threshold must be 1.0 or less.");

  ThresholdCount = (unsigned)ceil((src_mols.size()) * Parameters.Threshold) -
                   1;      // minimal required number of matched targets
  if (ThresholdCount < 1)  // at least one target
    ThresholdCount = 1;
  if (ThresholdCount > src_mols.size() - 1)  // max all targets
    ThresholdCount = src_mols.size() - 1;

  // Selecting CompleteRingsOnly option also enables --ring-matches-ring-only.
  // ring--ring and chain bonds only match chain bonds.
  if (Parameters.BondCompareParameters.CompleteRingsOnly)
    Parameters.BondCompareParameters.RingMatchesRingOnly = true;

  for (std::vector<ROMOL_SPTR>::const_iterator it = src_mols.begin();
       it != src_mols.end(); it++) {
    Molecules.push_back((*it).get());
    if (!Molecules.back()->getRingInfo()->isInitialized())
      Molecules.back()->getRingInfo()->initialize();  // but do not fill out !!!
  }

  // sort source set of molecules by their 'size' and assume the smallest
  // molecule as a query
  std::stable_sort(Molecules.begin(), Molecules.end(), molPtr_NumBondLess);

  for (size_t i = 0; i < Molecules.size() - ThresholdCount && !res.Canceled;
       i++) {
    init();
    if (Targets.empty()) break;
    MCSFinalMatchCheckFunction tff = Parameters.FinalMatchChecker;
    if (FinalChiralityCheckFunction == Parameters.FinalMatchChecker)
      Parameters.FinalMatchChecker = 0;  // skip final chirality check for
                                         // initial seed to allow future growing
                                         // of it
    makeInitialSeeds();
    Parameters.FinalMatchChecker = tff;  // restore final functor

    if (Parameters.Verbose)
      std::cout << "Query " << MolToSmiles(*QueryMolecule) << " "
                << QueryMolecule->getNumAtoms() << "("
                << QueryMoleculeMatchedAtoms << ") atoms, "
                << QueryMolecule->getNumBonds() << "("
                << QueryMoleculeMatchedBonds << ") bonds\n";

    if (Seeds.empty()) break;
    res.Canceled = growSeeds() ? false : true;
    // verify what MCS is equal to one of initial seed for chirality match
    if (FinalChiralityCheckFunction == Parameters.FinalMatchChecker &&
        1 == getMaxNumberBonds()) {
      McsIdx = MCS();      // clear
      makeInitialSeeds();  // check all possible initial seeds
      if (!Seeds.empty()) {
        const Seed& fs = Seeds.front();
        McsIdx.QueryMolecule = QueryMolecule;
        McsIdx.Atoms = fs.MoleculeFragment.Atoms;
        McsIdx.Bonds = fs.MoleculeFragment.Bonds;
        McsIdx.AtomsIdx = fs.MoleculeFragment.AtomsIdx;
        McsIdx.BondsIdx = fs.MoleculeFragment.BondsIdx;
      }

    } else if (i + 1 < Molecules.size() - ThresholdCount) {
      Seed seed;
      if (createSeedFromMCS(i, seed))  // MCS is matched with new query
        Seeds.push_back(seed);
      std::swap(Molecules[0],
                Molecules[i + 1]);  // change query molecule for threshold < 1.
    }
  }

  res.NumAtoms = getMaxNumberAtoms();
  res.NumBonds = getMaxNumberBonds();
  if (res.NumBonds > 0) res.SmartsString = generateResultSMARTS(McsIdx);

#ifdef VERBOSE_STATISTICS_ON
  if (Parameters.Verbose) {
    unsigned itarget = 0;
    for (std::vector<Target>::const_iterator tag = Targets.begin();
         res.NumAtoms > 0 && tag != Targets.end(); tag++, itarget++) {
      MatchVectType match;
      RWMol* m = SmartsToMol(res.SmartsString.c_str());

      bool target_matched = SubstructMatch(*tag->Molecule, *m, match);
      if (!target_matched)
        std::cout << "Target " << itarget + 1
                  << (target_matched ? " matched " : " MISMATCHED ")
                  << MolToSmiles(*tag->Molecule) << "\n";
      delete m;
    }

    std::cout << "STATISTICS:\n";
    std::cout << "Total Growing Steps  = " << VerboseStatistics.TotalSteps
              << ", MCS found on " << VerboseStatistics.MCSFoundStep << " step";
    if (VerboseStatistics.MCSFoundTime - To > 0)
      printf(", for %.4lf seconds\n",
             double(VerboseStatistics.MCSFoundTime - To) / 1000000.);
    else
      std::cout << ", for less than 1 second\n";
    std::cout << "Initial   Seeds      = " << VerboseStatistics.InitialSeed
              << ",  Mismatched " << VerboseStatistics.MismatchedInitialSeed
              << "\n";
    std::cout << "Inspected Seeds      = " << VerboseStatistics.Seed << "\n";
    std::cout << "Rejected by BestSize = "
              << VerboseStatistics.RemainingSizeRejected << "\n";
    std::cout << "SingleBondExcluded   = "
              << VerboseStatistics.SingleBondExcluded << "\n";
#ifdef EXCLUDE_WRONG_COMPOSITION
    std::cout << "Rejected by WrongComposition = "
              << VerboseStatistics.WrongCompositionRejected << " [ "
              << VerboseStatistics.WrongCompositionDetected << " Detected ]\n";
#endif
    std::cout << "MatchCheck Seeds     = " << VerboseStatistics.SeedCheck
              << "\n";
    std::cout  //<< "\n"
        << "     MatchCalls = " << VerboseStatistics.MatchCall << "\n"
        << "     MatchFound = " << VerboseStatistics.MatchCallTrue << "\n";
    std::cout << " fastMatchCalls = " << VerboseStatistics.FastMatchCall << "\n"
              << " fastMatchFound = " << VerboseStatistics.FastMatchCallTrue
              << "\n";
    std::cout << " slowMatchCalls = "
              << VerboseStatistics.MatchCall -
                     VerboseStatistics.FastMatchCallTrue << "\n"
              << " slowMatchFound = " << VerboseStatistics.SlowMatchCallTrue
              << "\n";

#ifdef VERBOSE_STATISTICS_FASTCALLS_ON
    std::cout << "AtomFunctorCalls = " << VerboseStatistics.AtomFunctorCalls
              << "\n";
    std::cout << "BondCompareCalls = " << VerboseStatistics.BondCompareCalls
              << "\n";
#endif
    std::cout << "  DupCacheFound = " << VerboseStatistics.DupCacheFound
              << "   " << VerboseStatistics.DupCacheFoundMatch << " matched, "
              << VerboseStatistics.DupCacheFound -
                     VerboseStatistics.DupCacheFoundMatch << " mismatched\n";
#ifdef FAST_SUBSTRUCT_CACHE
    std::cout << "HashCache size  = " << HashCache.keyssize() << " keys\n";
    std::cout << "HashCache size  = " << HashCache.fullsize() << " entries\n";
    std::cout << "FindHashInCache = " << VerboseStatistics.FindHashInCache
              << "\n";
    std::cout << "HashFoundInCache= " << VerboseStatistics.HashKeyFoundInCache
              << "\n";
    std::cout << "ExactMatchCalls = " << VerboseStatistics.ExactMatchCall
              << "\n"
              << "ExactMatchFound = " << VerboseStatistics.ExactMatchCallTrue
              << "\n";
#endif
  }
#endif

  clear();
  return res;
}

bool MaximumCommonSubgraph::checkIfMatchAndAppend(Seed& seed) {
#ifdef VERBOSE_STATISTICS_ON
  ++VerboseStatistics.SeedCheck;
#endif
#ifdef FAST_SUBSTRUCT_CACHE
  SubstructureCache::HashKey cacheKey;
  SubstructureCache::TIndexEntry* cacheEntry = 0;
  bool cacheEntryIsValid = false;
  RDUNUSED_PARAM(cacheEntryIsValid);  // unused var
#endif

  bool foundInCache = false;
  bool foundInDupCache = false;

  {
#ifdef DUP_SUBSTRUCT_CACHE
    if (DuplicateCache.find(seed.DupCacheKey, foundInCache)) {
// duplicate found. skip match() but store both seeds, because they will grow by
// different paths !!!
#ifdef VERBOSE_STATISTICS_ON
      VerboseStatistics.DupCacheFound++;
      VerboseStatistics.DupCacheFoundMatch += foundInCache ? 1 : 0;
#endif
      if (!foundInCache)  // mismatched !!!
        return false;
    }
    foundInDupCache = foundInCache;
#endif
#ifdef FAST_SUBSTRUCT_CACHE
    if (!foundInCache) {
#ifdef VERBOSE_STATISTICS_ON
      ++VerboseStatistics.FindHashInCache;
#endif
      cacheEntry =
          HashCache.find(seed, QueryAtomLabels, QueryBondLabels, cacheKey);
      cacheEntryIsValid = true;
      if (cacheEntry) {  // possibly found. check for hash collision
#ifdef VERBOSE_STATISTICS_ON
        ++VerboseStatistics.HashKeyFoundInCache;
#endif
        // check hash collisions (time +3%):
        for (SubstructureCache::TIndexEntry::const_iterator g =
                 cacheEntry->begin();
             !foundInCache && g != cacheEntry->end(); g++) {
          if (g->m_vertices.size() != seed.getNumAtoms() ||
              g->m_edges.size() != seed.getNumBonds())
            continue;
#ifdef VERBOSE_STATISTICS_ON
          ++VerboseStatistics.ExactMatchCall;
#endif
          // EXACT MATCH
          foundInCache = SubstructMatchCustomTable(
              (*g), *QueryMolecule, seed.Topology, *QueryMolecule,
              QueryAtomMatchTable, QueryBondMatchTable, &Parameters);
#ifdef VERBOSE_STATISTICS_ON
          if (foundInCache) ++VerboseStatistics.ExactMatchCallTrue;
#endif
        }
      }
    }
#endif
  }
  bool found = foundInCache;

  if (!found) {
    found = match(seed);
  }

  Seed* newSeed = 0;

  {
    if (found) {  // Store new generated seed, if found in cache or in all(-
                  // threshold) targets
      {
        newSeed = &Seeds.add(seed);
        newSeed->CopyComplete = false;
      }

#ifdef DUP_SUBSTRUCT_CACHE
      if (!foundInDupCache && seed.getNumBonds() >= 3)  // only seed with a ring
                                                        // can be duplicated -
                                                        // do not store very
                                                        // small seed in cache
        DuplicateCache.add(seed.DupCacheKey, true);
#endif
#ifdef FAST_SUBSTRUCT_CACHE
      if (!foundInCache) HashCache.add(seed, cacheKey, cacheEntry);
#endif
    } else {
#ifdef DUP_SUBSTRUCT_CACHE
      if (seed.getNumBonds() > 3)
        DuplicateCache.add(seed.DupCacheKey,
                           false);  // opt. cache mismatched duplicates too
#endif
    }
  }
  if (newSeed)
    *newSeed =
        seed;  // non-blocking copy for MULTI_THREAD and best CPU utilization

  return found;  // new matched seed has been actualy added
}

bool MaximumCommonSubgraph::match(Seed& seed) {
  unsigned max_miss = Targets.size() - ThresholdCount;
  unsigned missing = 0;
  unsigned passed = 0;
  unsigned itarget = 0;

  for (std::vector<Target>::const_iterator tag = Targets.begin();
       tag != Targets.end(); tag++, itarget++) {
#ifdef VERBOSE_STATISTICS_ON
    { ++VerboseStatistics.MatchCall; }
#endif
    bool target_matched = false;
    if (!seed.MatchResult.empty() && !seed.MatchResult[itarget].empty())
      target_matched = matchIncrementalFast(seed, itarget);
    if (!target_matched) {  // slow full match
      match_V_t match;      // THERE IS NO Bonds match INFO !!!!
      target_matched = SubstructMatchCustomTable(
          tag->Topology, *tag->Molecule, seed.Topology, *QueryMolecule,
          tag->AtomMatchTable, tag->BondMatchTable, &Parameters, &match);
      // save current match info
      if (target_matched) {
        if (seed.MatchResult.empty()) seed.MatchResult.resize(Targets.size());
        seed.MatchResult[itarget].init(seed, match, *QueryMolecule, *tag);
      } else if (!seed.MatchResult.empty())
        seed.MatchResult[itarget].clear();  //.Empty = true; // == fast clear();
#ifdef VERBOSE_STATISTICS_ON
      if (target_matched) {
        ++VerboseStatistics.SlowMatchCallTrue;
      }
#endif
    }

    if (target_matched) {
      if (++passed >= ThresholdCount)  // it's enought
        break;
    } else {  // mismatched
      if (++missing > max_miss) break;
    }
  }
  if (missing <= max_miss) {
#ifdef VERBOSE_STATISTICS_ON
    ++VerboseStatistics.MatchCallTrue;
#endif
    return true;
  }
  return false;
}

// call it for each target, if failed perform full match check
bool MaximumCommonSubgraph::matchIncrementalFast(Seed& seed, unsigned itarget) {
// use and update results of previous match stored in the seed
#ifdef VERBOSE_STATISTICS_ON
  { ++VerboseStatistics.FastMatchCall; }
#endif
  const Target& target = Targets[itarget];
  TargetMatch& match = seed.MatchResult[itarget];
  if (match.empty()) return false;
  /*
  // CHIRALITY: FinalMatchCheck:
  if(Parameters.AtomCompareParameters.MatchChiralTag ||
  Parameters.FinalMatchChecker) {   // TEMP
          match.clear();
          return false;
  }
  */
  bool matched = false;
  for (unsigned newBondSeedIdx = match.MatchedBondSize;
       newBondSeedIdx < seed.getNumBonds(); newBondSeedIdx++) {
    matched = false;
    bool atomAdded = false;
    const Bond* newBond = seed.MoleculeFragment.Bonds[newBondSeedIdx];
    unsigned newBondQueryIdx = seed.MoleculeFragment.BondsIdx[newBondSeedIdx];

    unsigned newBondSourceAtomSeedIdx;   // seed's index of atom from which new
                                         // bond was added
    unsigned newBondAnotherAtomSeedIdx;  // seed's index of atom on another end
                                         // of the bond
    unsigned i =
        seed.MoleculeFragment.SeedAtomIdxMap[newBond->getBeginAtomIdx()];
    unsigned j = seed.MoleculeFragment.SeedAtomIdxMap[newBond->getEndAtomIdx()];
    if (i >= match.MatchedAtomSize) {  // this is new atom in the seed
      newBondSourceAtomSeedIdx = j;
      newBondAnotherAtomSeedIdx = i;
    } else {
      newBondSourceAtomSeedIdx = i;
      newBondAnotherAtomSeedIdx = j;
    }
    unsigned newBondAnotherAtomQueryIdx =
        seed.MoleculeFragment.AtomsIdx[newBondAnotherAtomSeedIdx];
    unsigned newBondSourceAtomQueryIdx =
        seed.MoleculeFragment.AtomsIdx[newBondSourceAtomSeedIdx];
    unsigned newBondSourceAtomTargetIdx =
        match.TargetAtomIdx
            [newBondSourceAtomQueryIdx];  // matched to newBondSourceAtomSeedIdx

    const Bond* tb = NULL;
    unsigned newBondAnotherAtomTargetIdx = NotSet;

    if (newBondAnotherAtomSeedIdx <
        match.MatchedAtomSize) {  // new bond between old atoms - both are
                                  // matched to exact atoms in the target
      newBondAnotherAtomTargetIdx =
          match.TargetAtomIdx[newBondAnotherAtomQueryIdx];
      tb = target.Molecule->getBondBetweenAtoms(
          newBondSourceAtomTargetIdx,
          newBondAnotherAtomTargetIdx);  // target bond between Source and
                                         // Another atoms
      if (tb) {  // bond exists, check match with query molecule
        unsigned tbi = tb->getIdx();
        unsigned qbi = seed.MoleculeFragment.BondsIdx[newBondSeedIdx];
        if (!match.VisitedTargetBonds[tbi])  // false if target bond is already
                                             // matched
          matched = target.BondMatchTable.at(qbi, tbi);
      }
    } else {  // enumerate all bonds from source atom in the target
      const Atom* atom =
          target.Molecule->getAtomWithIdx(newBondSourceAtomTargetIdx);
      ROMol::OEDGE_ITER beg, end;
      for (boost::tie(beg, end) = target.Molecule->getAtomBonds(atom);
           beg != end; beg++) {
        tb = &*((*target.Molecule)[*beg]);
        if (!match.VisitedTargetBonds[tb->getIdx()]) {
          newBondAnotherAtomTargetIdx = tb->getBeginAtomIdx();
          if (newBondSourceAtomTargetIdx == newBondAnotherAtomTargetIdx)
            newBondAnotherAtomTargetIdx = tb->getEndAtomIdx();

          if (newBondAnotherAtomSeedIdx <
                  seed.LastAddedAtomsBeginIdx  // RING: old atom, new atom in
                                               // matched substructure must be
                                               // new in seed
              ||
              std::find(seed.MoleculeFragment.AtomsIdx.begin() +
                            seed.LastAddedAtomsBeginIdx,
                        seed.MoleculeFragment.AtomsIdx.begin() +
                            newBondAnotherAtomSeedIdx,
                        newBondAnotherAtomQueryIdx) ==
                  seed.MoleculeFragment.AtomsIdx.end()) {
            if (!match.VisitedTargetAtoms[newBondAnotherAtomTargetIdx])
              continue;
          } else {
            if (match.VisitedTargetAtoms[newBondAnotherAtomTargetIdx]) continue;
          }

          // check AnotherAtom and bond
          matched =
              target.AtomMatchTable.at(newBondAnotherAtomQueryIdx,
                                       newBondAnotherAtomTargetIdx) &&
              target.BondMatchTable.at(
                  seed.MoleculeFragment.BondsIdx[newBondSeedIdx], tb->getIdx());

          if (matched) {
            atomAdded = true;
            break;
          }
        }
      }
    }

    if (matched) {      // update match history
      if (atomAdded) {  // new atom has been added
        match.MatchedAtomSize++;
        match.TargetAtomIdx[newBondAnotherAtomQueryIdx] =
            newBondAnotherAtomTargetIdx;
        match.VisitedTargetAtoms[newBondAnotherAtomTargetIdx] = true;
      }
      match.MatchedBondSize++;
      match.TargetBondIdx[newBondQueryIdx] = tb->getIdx();
      match.VisitedTargetBonds[tb->getIdx()] = true;
    } else {
      match.clear();
      return false;
    }
  }

  if (match.MatchedAtomSize != seed.getNumAtoms() ||
      match.MatchedBondSize !=
          seed.getNumBonds()) {  // number of unique items !!!
    match.clear();
    return false;
  }
  // CHIRALITY: FinalMatchCheck
  if (matched && Parameters.FinalMatchChecker) {
    short unsigned c1[4096];  // seed.getNumAtoms()
    short unsigned c2[4096];  // seed.getNumAtoms()
    for (unsigned si = 0; si < seed.getNumAtoms();
         si++) {  // index in the seed topology
      c1[si] = si;
      c2[si] = match.TargetAtomIdx[seed.Topology[si]];
    }
    matched = Parameters.FinalMatchChecker(
        c1, c2, *QueryMolecule, seed.Topology, *target.Molecule,
        target.Topology, &Parameters);  // check CHIRALITY
    if (!matched) match.clear();
  }
#ifdef VERBOSE_STATISTICS_ON
  if (matched) {
#ifdef MULTI_THREAD
    Guard statlock(StatisticsMutex);
#endif
    ++VerboseStatistics.FastMatchCallTrue;
  }
#endif
  return matched;
}
}
}  // namespace RDKit
